A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa
A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa
复制标题
水稻小核仁 RNA 和可能的中等大小非编码 RNA 的整体鉴定和分析
DOI：
10.1093/mp/sss087
复制
发表时间：
2013-05-01
期刊：
影响因子：
27.5
通讯作者：
Deng, Xing Wang
中科院分区：
文献类型：
--
作者：
Liu, Ting-Ting;Zhu, Danmeng;Deng, Xing Wang
越来越多的证据表明，非编码RNA(NcRNAs)在许多真核生物中既广泛存在，又具有重要的功能。在本研究中，我们采用了一种特殊的大小分离和构建文库的方法，然后进行了454深度测序，系统地描述了水稻中等大小的ncRNAs。我们的分析共鉴定了1349个ncRNAs，其中包括754个未知功能类别的新ncRNAs。所有已鉴定的ncRNAs的染色体分布没有链偏向，并且显示出与蛋白质编码基因相似的模式，几乎没有染色体依赖性。超过一半的ncRNA集中在编码区5和3末端的正链周围。大多数新的ncRNAs是水稻特有的，而78%的小核仁RNAs(SnoRNAs)是保守的。串联复制推动了超过一半的snoRNA基因家族的扩张。此外，90%的候选snoRNA在2030年核苷酸之间产生小RNA，其中80%一般与ArgAert蛋白有关，特别是AGO1b。总体而言，我们的发现提供了单子叶物种中中等大小的非编码转录组的综合视图，这将为深入分析ncRNA功能提供一个有用的平台。
Accumulating evidence suggests that non-coding RNAs (ncRNAs) are both widespread and functionally important in many eukaryotic organisms. In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5 and 3 termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs (snoRNAs) were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 2030 nt, 80% of which were associated with ARGONAUT proteins generally, and AGO1b in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.